You always check in with the airline that operates the flight you're about to board. Their staff knows what other flight numbers it was sold as and are used to seeing bookings under those numbers. They will give you as many boarding passes as they can. Those may or may not cover the rest of your journey. If you need more boarding passes for later flights, you get them with whatever airline operates the first flight you need another boarding pass for, at the airport where you will board that flight.